Principal Scientist, Antigen Engineering & Production

The Institute for Protein Innovation (IPI)is a nonprofit research organization advancing protein science to accelerate research and improve human health.  Founded in 2017 and located in Boston’s Longwood Medical Area, the Institute’s three-pronged strategy is to build protein tools, conduct related internal research and develop educational programs for the protein science and biological research communities.

With a significant endowment, IPI uniquely combines the freedom of academia with the high throughput and scale of industry to take on transformative projects. IPI has built a robust platform for discovering, developing, and distributing synthetic antibodies and other protein tools to share with the biomedical community. The Institute's deep protein expertise, collaborative spirit and research tools are powering new biomedical and therapeutic discoveries with a growing community of researchers at Harvard Medical School, Boston Children's Hospital and other institutions across Greater Boston and beyond.  

Position Summary

The Institute for Protein Innovation (IPI) seeks an enthusiastic and experienced Principal Scientist to lead our Antibody Engineering and Production team. The successful candidate will specialize in high-throughput antibody expression across various systems, with a focus in developing flexible and scalable methods to produce and purify large numbers of biomolecules in different formats (human and rabbit IgG, Fab, VHH, miniproteins, bispecifics, biparatopics, and others). The Principal Scientist will also contribute to IPI’s expertise in protein science, helping to develop expression, purification, and formulation strategies for multiple types of proteins, including the antigens used for discovery.

Position Overview

As a critical leader within the Antibody Platform, Principal Scientist, Antigen Engineering & Production manages the day-to-day operations of IPI’s high-throughput antigen production pipeline, ensuring seamless integration with downstream antibody discovery and characterization workflows. The incumbent drives high-throughput protein design, expression, purification, and characterization strategies and establishes efficient systems and data infrastructure to accelerate research programs. Beyond internal operations, this position leads high-impact projects, cultivate external collaborations, and contributes to the global scientific community through grants and publications.

Primary Responsibilities

High-Throughput Technical Strategy:

• High-Throughput Antigen Engineering: Apply structure-based design approaches using structural biology tools and computational modeling (e.g., AlphaFold) for protein engineering and construct design at scale.
• Expression Optimization: Design and execute high-throughput expression experiments for a wide range of protein targets across mammalian cells (CHO, HEK293), bacteria, and yeast.
• Scalable Purification: Perform and optimize high-throughput purification strategies using techniques such as affinity chromatography, ion-exchange chromatography, and size-exclusion chromatography (SEC).
• Quality & Analysis: Conduct thorough protein characterization using analytical techniques, including HPLC, SEC, Dynamic Light Scattering (DLS), and SDS-PAGE, to ensure the quality and integrity of protein samples. Troubleshoot and resolve challenges related to protein purity, yield, and stability.

Leadership, Operations & Scientific Engagement:

• Team & Pipeline Management: Lead and mentor a team of high-performing team research associates. Manage the day-to-day operations of the high-throughput antigen production pipeline, ensuring it efficiently serves the needs of the Antibody Platform's discovery and characterization workflows.
• Strategic Operations: Define KPIs, experimental priorities, and project timelines to ensure efficient program execution and high-throughput scaling.
• Infrastructure Development: Implement scalable workflows and collaborate across discovery, validation, bioinformatics, and automation teams to establish efficient high-throughput systems.
• Project & Collaboration Leadership: Serve as the primary lead for complex protein engineering projects. Engage with outside academic and industry collaborators to translate their biological questions into novel protein reagents.
• Scientific Contribution & Grants: Share reagents and findings with the larger research community through abstracts, presentations, and publications. Take a leadership role in writing research papers and securing funding through grant proposals.

Qualifications

• Ph.D. in Biochemistry, Structural Biology, Molecular Biology, Bioengineering, or a closely related scientific discipline.
• 5 years of post-doctoral or industry experience, demonstrating a clear progression into scientific leadership and laboratory management.
• Demonstrated success in driving scientific output, including a strong portfolio of peer-reviewed research papers and experience securing funding through grant proposals.
• Familiarity with structural biology techniques and applications, including construct design and the use of computational modeling (e.g., AlphaFold).

• Deep expertise and well acquainted with best practices in cell culture and recombinant protein reagent production, specifically scaling mammalian (CHO, HEK293) and bacterial expression systems for high-throughput environments.
• Good organizational and documentation skills, essential for managing pipeline metrics, project timelines, and high-throughput data infrastructure.
• Excellent problem-solving skills and the ability to work independently as well as in a team environment.

• Strong written and verbal communication skills with the ability to convey complex scientific concepts clearly to cross-functional teams and external industry/academic collaborators.
• Proven track record of directly managing research associates, mentoring scientists, and overseeing complex, high-throughput pipeline operations.
• Ability to work in a fast-paced, intellectually challenging environment.
• Enthusiastic team member with a strong commitment to the Institute's open-science mission and a desire to conduct highly impactful science.

IPI provides competitive compensation and an excellent benefits package to support physical, mental and financial health. Highlights of benefits include:

·        100% employer-paid medical, dental, and vision plans

·        Flexible spending accounts and a healthcare reimbursement account

·        401(k) plan with generous 6% employer match – immediately 100% vested

·        Generous PTO package

·        Commuter and parking reimbursement

·        Career development opportunities

For more information, visit proteininnovation.org or follow us on social media, @ipiproteins. IPI is an independent 501(c)(3) nonprofit research organization and an equal-opportunity employer. The Institute celebrates diversity and is committed to creating an inclusive environment for all employees. Please be advised that you will be required to provide evidence of your identity and eligibility for employment in the United States. IPI will not guarantee sponsorship of foreign nationals and retains complete discretion regarding providing sponsorship to any prospective or existing employee at time of hire or at any time in the future.

Salary : $145,000 - $175,000